[BioSQL-l] [BioPython] BioSQL : GenBank db_xref names in dbxref table

[Peter]

Thank you Chris and Mauricio,

On 11/23/07, Chris Fields <cjfields at uiuc.edu> wrote:
> I think [BioPerl's] SeqIO checks the name for parsing reasons only, in
> cases where the format changes based on the source (such as GenPept
> DBSOURCE data).  I don't think we go beyond that in Bioperl, probably
> b/c modifying or expanding names for data persistence would lead to
> volatile coding issues (i.e. consistency between parsers, constant
> updating to cover new crossrefs, etc).

And in Biopython's case, we get annoying warnings if it hasn't seen
the term before!  Which is way I filed Biopython bug 2405 in the first
place :)
http://bugzilla.open-bio.org/show_bug.cgi?id=2405

> I would definitely suggest retaining the original DB as it appears in
> the dbxref for consistency/sanity; if needed return expanded names
> using a different method if they are designated.

Sounds good to me.

Peter